UC Davis News: Research

100K Pathogen Genome Project maps first genomes

Tue, 21 May 2013 11:00:00 -0700

Striking a blow at foodborne diseases, the 100K Pathogen Genome Project at the University of California, Davis, today announced that it has sequenced the genomes of its first 10 infectious microorganisms, including strains of Salmonella and Listeria.

“We are creating a free, online encyclopedia or reference database of genomes so that during a foodborne disease outbreak, scientists and public health professionals can quickly identify the responsible microorganism and track its source in the food supply using automated information-handling methods,” said Professor Bart Weimer, director of the 100K Genome Project and co-director of BGI@UC Davis, the Sacramento facility where the sequencing is carried out.

Weimer estimates that the availability of this genomic information will cut in half the time necessary to diagnose and treat foodborne illnesses, and will enable scientists to make discoveries that can be used to develop new methods for controlling disease-causing microorganisms in the food chain.

The project is dedicated to sequencing the genomes of 100,000 bacteria and viruses that cause serious foodborne illnesses in people around the world.

In the United States alone, foodborne diseases annually sicken 48 million people and kill 3,000, according to the Centers for Disease Control and Prevention.

The initial 10 genome sequences mark the first in a series that the project will enter into a publicly available database at the National Center for Biotechnology Information of the National Institutes of Health.

“This initial release validates the entire process, from start to finish, of acquiring the bacterium, producing the genome sequence, and making automated public releases,” Weimer said.

A genome is the complete collection of an organism’s hereditary information.

Weimer said that the 100K Genome Project currently is sequencing a second set of 1,500 microbial genomes, with an anticipated release in the fall of 2013.

About the 100K Genome Project

The 100K Genome Project was launched in March 2012 as a collaborative effort between UC Davis, Agilent Technologies, and the U.S. Food and Drug Administration. Since then, the U.S. Centers for Disease Control and Prevention, Department of Agriculture, and National Institutes of Health, as well as seven corporate partners, have joined the worldwide effort.

Iron-platinum alloys could be new-generation hard drives

Mon, 20 May 2013 11:48:00 -0700

Meeting the demand for more data storage in smaller volumes means using materials made up of ever-smaller magnets, or nanomagnets. One promising material for a potential new generation of recording media is an alloy of iron and platinum with an ordered crystal structure. Researchers led by Professor Kai Liu and graduate student Dustin Gilbert at the University of California, Davis, have now found a convenient way to make these alloys and tailor their properties.

"The relatively convenient synthesis conditions, along with the tunable magnetic properties, make these materials highly desirable for future magnetic recording technologies," said Liu, a professor of physics. The iron-platinum alloy has the ability to retain information even at extremely small nanomagnet sizes, and it is resistant to heat effects.

Previous methods for making the iron-platinum alloys with an ordered crystal structure involved high-temperature treatments that would be difficult to integrate into the rest of the manufacturing process, Liu said.

The researchers, including Liang-Wei Wang and Chih-Huang Lai of the National Tsing Hua University, Taiwan, and Timothy Klemmer and Jan-Ulrich Thiele, of Seagate Technologies in Fremont, used a method called atomic-scale multilayer sputtering to create a material with extremely thin layers of metal, and rapid thermal annealing to convert it into the desirable ordered alloy. They were able to adjust the magnetic properties of the alloy by adding small amounts of copper into particular regions of the alloy.

A paper describing the work was recently published in the journal Applied Physics Letters and featured in its Research Highlights. The work was supported by the National Science Foundation Materials World Network Program.

Non-wetting fabric drains sweat

Mon, 20 May 2013 11:48:00 -0700

Waterproof fabrics that whisk away sweat could be the latest application of microfluidic technology developed by bioengineers at the University of California, Davis.

The new fabric works like human skin, forming excess sweat into droplets that drain away by themselves, said inventor Tingrui Pan, professor of biomedical engineering. One area of research in Pan's Micro-Nano Innovations Laboratory at UC Davis is a field known as microfluidics, which focuses on making "lab on a chip" devices that use tiny channels to manipulate fluids. Pan and his colleagues are developing such systems for applications like medical diagnostic tests.

Graduate students Siyuan Xing and Jia Jiang developed a new textile microfluidic platform using hydrophilic (water-attracting) threads stitched into a highly water-repellent fabric. They were able to create patterns of threads that suck droplets of water from one side of the fabric, propel them along the threads and expel them from the other side.

"We intentionally did not use any fancy microfabrication techniques so it is compatible with the textile manufacturing process and very easy to scale up," said Xing, lead graduate student on the project.

It's not just that the threads conduct water through capillary action. The water-repellent properties of the surrounding fabric also help drive water down the channels. Unlike conventional fabrics, the water-pumping effect keeps working even when the water-conducting fibers are completely saturated, because of the sustaining pressure gradient generated by the surface tension of droplets.

The rest of the fabric stays completely dry and breathable. By adjusting the pattern of water-conducting fibers and how they are stitched on each side of the fabric, the researchers can control where sweat is collected and where it drains away on the outside.

Workout enthusiasts, athletes and clothing manufacturers are all interested in fabrics that remove sweat and let the skin breathe. Cotton fibers, for example, wick away sweat — but during heavy exercise, cotton can get soaked, making it clingy and uncomfortable.

A paper describing the research was published recently in the journal Lab on a Chip. The work was funded in part by the National Science Foundation.

UC Davis startup changes listening experience

Mon, 20 May 2013 10:30:00 -0700

Fifteen years of research at the University of California, Davis, is being turned into commercial products by Dysonics, a startup company based in San Francisco. Since becoming the first "graduate" from the Engineering Translational Technology Center, a technology incubator at the UC Davis College of Engineering, Dysonics has launched an iPhone app and is developing a broad product range for future launch. The company currently has 10 employees.

Dysonics aims to reproduce a natural sound experience with sound delivered through headphones. The Rondo iPhone app can change the apparent size of the room, and adds directionality. Add the RondoMotion sensor clipped to your headphones, and sounds will appear to change location as you move your head.

The Rondo app and RondoMotion work with existing audio files. The company is also working on generating its own content by recording live events on specialized media. The technology has promise not just for listening to recorded music in a new and richer way, but for a more realistic, "virtual reality" audio experience for teleconferencing and video games.

"There are multiple applications with market potential," said David McGee, executive director of InnovationAccess, the unit within the UC Davis Office of Research responsible for intellectual property management and licensing. "Dysonics is a great example of a faculty-led startup with cool technology and very active support from the college and university."

UC Davis played a crucial role in getting Dysonics started, said co-founder and President Ralph Algazi, professor emeritus of electrical and computer engineering at UC Davis. The company is based on research conducted at UC Davis by Algazi and co-founders Richard Duda, a research scientist at UC Davis, Robert Dalton Jr., a former undergraduate and graduate student in Algazi's lab, and colleagues at the university over several years.

Algazi is interested in how sound waves arriving at our ears carry information, for example, about the size and shape of the room or the direction of the sound source. For example, a piece of music sounds different played in a concert hall or on home theater system than it does played in a small room, or over ear buds. If we turn our heads toward a sound source, our experience changes.

Starting about 10 years ago, the team developed software and equipment that allows motion tracking with headphones, so that when you move your head the sound source appears to stay in the same place.

Algazi was one of the first inventors that McGee met with when he arrived on campus in 2004.

"Ralph gave me a demonstration of the technology, and I was just blown away," McGee said. "This was an entirely different and richer audio experience from what I was used to."

InnovationAccess worked with Algazi and licensed the technology to an existing company. But changing business priorities took that company in a different direction, and UC Davis took the license back so as to ensure that this promising technology would not languish.

By the end of the decade several trends were converging that would lead to the formation of Dysonics.

Motion-sensing technology has become much cheaper and more mobile. At the same time, the boom in mobile devices means people want to be able to listen to music wherever they are, setting off explosive growth in the market for headphones.

"When Ralph told me that he had decided to move the technology forward himself, I was very pleased and we worked very closely with him to make it happen," McGee said. "Empowering an entrepreneurial campus researcher to turn their research into societal impact is what technology transfer is all about."

Algazi talked to Bruce White, then dean of engineering, and ETTC director Jim Olson, a former undergraduate student of Algazi's. The company was founded in March 2011, and just over a year later had secured sufficient funding from angel investors to leave the incubator and strike out on its own.

"ETTC was invaluable for us in securing funding and legal work," Dalton said. "We had a heavy engineering focus and we needed business knowledge."

One unique feature of the ETTC incubator is that philanthropic donations to the College of Engineering enable it to reduce initial patent costs for startup companies. Filing patents costs the university money. Usually, when a company licenses a patent from UC Davis, it agrees to reimburse these out-of-pocket costs as well as support future ongoing costs of maintaining the licensed patents.

"ETTC is able to directly reimburse the university for up to $15,000 in patent costs. The ETTC startup is not charged for those costs. This is enormously beneficial to startups at a stage when they have very little cash," McGee said.

It also permits the startup to secure its foundational intellectual property, a very important consideration for investors. UC Davis Chancellor Linda P.B. Katehi recently approved the use of income from licensing intellectual property to maintain ETTC's ability to cover these costs.

The young company also worked with InnovationAccess to license the patents held by UC Davis.

The company recently (April 24) launched a "kickstarter" campaign to raise funds for its next product, a wireless motion sensor for audio headphones that works with the company's Rondo iPhone app. The company aims to raise $60,000 from the fundraising drive to complete the product.

More than 45 startup companies have been spun off from UC Davis since 2005. The campus currently holds a portfolio of 838 foreign and U.S. patents, and earned income of $13.6 million in fiscal year 2011-12.

Don’t lose the organism in the excitement over its genes, biologists urge

Mon, 20 May 2013 00:00:00 -0700

It’s been said metaphorically that too much focus on the trees can cause one to lose sight of the forest. In a similar check of perspective, a group of biologists, led by a University of California, Davis, scientist, suggests that decades of focus on genes has led the scientific community away from a balanced exploration of the organisms that those genes define — whether they be plants, animals or microorganisms.

In an article appearing this week in the June issue of the journal BioScience, the researchers assert that genetic variation alone does not adequately explain the intricate variations in the physiology and behavior of complex organisms. They propose a renewed emphasis on studying individual organisms in the context of specific environments, considering in greater depth the unique environmental exposures and experiences over the course of these organisms’ lives.

“Biology’s strong focus on genes during the past 50 years has generated a solid foundation for studying the mechanisms that determine the phenotype — the structure and function — of living organisms,” said Dietmar Kueltz, a professor of physiological genomics in the UC Davis Department of Animal Science.

He noted that despite the wide-ranging practical implications, little is known about how such mechanisms are influenced by the unique lifelong sequence of environmental exposures experienced by individuals. For instance, individuals’ disease susceptibility, stress resilience, coping ability and other important performance traits, as well as complex behavioral patterns, decision making and human psychology are not only determined by genes but also greatly influenced by prior exposures, learning and life-history experiences.

“It is critical that we now emphasize more strongly the complementation of gene-oriented approaches with a renewed focus on the organismal phenotypes in the context of specific environments and life histories, in order to better understand and explain the physiology and behavior of such complex organisms,” Kueltz said.

Kueltz and his colleagues maintain that during the past several decades, biological research has moved away from the organism in two gene-focused directions: inward, toward the world of cellular and molecular biology, and outward, toward the broad-scale evolutionary issues of population and quantitative genetics.

“These two movements resulted in many monumental discoveries and advances that now define modern biology,” Kueltz said. “The challenge now is to make the most of the vast insights from those movements and develop a deeper understanding of how, for example, variations in individual physiological and behavioral traits influence ecological and evolutionary processes.”

He and his colleagues advise that a modern research emphasis on organismal phenotypes will require cross-fertilization and integration of traditionally disparate fields of biology, including developmental biology, physiology, morphology, behavioral biology, neuroscience, ecology and evolutionary biology.

They propose that improved tracking technologies are needed to record life-history exposures and experiences of complex organisms, as well as the environmental variables in their natural habitats at proper resolution. Furthermore, they call for accelerated development of more powerful and widely accessible high-throughput tools for elucidating the structure and function of organisms, just as high-throughput technology was created for comprehensive studies of genetic blueprints.

“There are promising developments under way in all of these areas,” Kueltz said. “We look forward to the advances in the biology of complex organisms that will be achieved when efforts in these technological and organizational areas are intensified.”

The BioScience article represents the analyses and discussions from a 2011 workshop in Arlington, Va., on the future of organismal biology, supported by the National Science Foundation.

Co-authors are: David F. Clayton and Gene E. Robinson, University of Illinois at Urbana-Champaign; Craig Albertson, University of Massachusetts, Amherst; Hannah V. Carey, University of Wisconsin, Madison; Molly E. Cummings, Hans A. Hofmann, and Daniel C. Stanzione, University of Texas, Austin; Ken Dewar and Michael J. Meaney, McGill University; Scott V. Edwards, Harvard University; Louis J. Gross, University of Tennessee, Knoxville; Joel G. Kingsolver, University of North Carolina at Chapel Hill; Barney A. Schlinger, University of California, Los Angeles; Alexander W. Shingleton, Michigan State University; Marla B. Sokolowski, University of Toronto; George N. Somero, Stanford University; and Anne E. Todgham, San Francisco State University.

New approach to heart valve replacement wins at Big Bang! business competition

Fri, 17 May 2013 13:05:00 -0700

A new approach to tissue preparation that makes heart valve replacements less likely to be rejected by the body’s immune system — potentially giving transplant patients longer, healthier lives — was the clear favorite in this year’s University of California, Davis, business plan competition — sweeping both the first prize and the People’s Choice award.

ViVita Technologies, a team comprising a UC Davis veterinarian and three biomedical engineering doctoral students, took home a total of $12,000 in the 13th annual Big Bang! Business Plan Competition, run by MBA students in the UC Davis Graduate School of Management: $10,000 for first place, decided by a team of judges, and $2,000 for the People’s Choice award, decided by a vote of the approximately 150 people who attended the awards ceremony Thursday evening (May 16) at the UC Davis Conference Center.

Second prize of $5,000 went to Davis Chem, a team that is working to commercialize a sustainable method of producing isobutryaldehyde, a common base chemical used in everything from paint to cosmetics, with genetically modified E. coli bacteria rather than with the petroleum products currently used in production.

ViVita Technologies was driven to create its product to address the current shortage of organs. “But unlike with current heart valve transplants, the patient would be free from a lifetime of drugs,” said Maelene Wong, chief executive officer of the nascent company.

The ViVita process removes substances that trigger patients’ immune response while preserving the structural integrity and functional properties of the replacement valve tissue. The method has been successfully tested on small animals, they said.

The proprietary process allows the patient’s own cells to join and grow with the transplant tissue — a process that the team says could eventually be used for any organ transplant. Such an organ transplant would allow the person to lead a normal, healthy life without fear of organ rejection and the need to spend a lifetime on anti-rejection medication. It would also allow for better transplant methods for children, who often need new transplants, and additional surgeries, when their bodies grow, Wong said.

She and two fellow biomedical engineers teamed with Leigh Griffiths, an assistant professor of cardiology and cardiac surgeon in the UC Davis School of Veterinary Medicine, to develop the technology. Last summer, they honed their business development skills to create ViVita through the Biomedical Engineering Entrepreneur Academy at the UC Davis Child Family Institute for Innovation and Entrepreneurship.

The second-place team of part-time MBA students initially thought of developing an application to monitor snowboarding velocity, but thought the better of it after learning of an existing UC Davis patent during a business development clinic last year. The patent is held by Shota Atsumi, an assistant professor of chemistry.

“We didn’t even know how to pronounce the chemical at first,” said MBA student Sandeep Deshpande. “Wil (Agatstein, the instructor) helped convince us that this existing patent was a better way to go.”

Said Agatstein, who is executive director of the Child Family Institute: “And they took the idea and ran with it.”

The team plans to use the money to start a pilot project next year.

This was the first time the five finalist teams included second-year undergraduates — a change Agatstein said is due to more undergraduates interested in entrepreneurship at an earlier age. That young team, AmberCycle, which includes Akshay Sethi, 19, a biochemical and molecular biology student, Matthew Remich, 20, a managerial economics student, and MBA student Gerald Dion, developed a system to degrade plastics so that they are cheaper and easier to recycle.

Andrew Hargadon, faculty director of the Child Family Institute, said he had seen a change in the volume and quality of Big Bang! entries, and expects many of them to become businesses in the community — as multiple winners from past years already have. “To see them morph from class projects into real businesses is truly terrific,” he said.

Roger Akers, of Akers Capital, who judges the competition each year, said he has seen vast change in the competition. “Every year the quality improves — and it’s not just the business plan, it’s the quality of the people and their projects. It’s wonderful to see.”

This year, the Big Bang! received a $50,000 gift from Andrew Barkett, an engineering manager at Facebook and a 2009 graduate of the Graduate School of Management.

About the UC Davis Child Family Institute for Innovation and Entrepreneurship

The UC Davis Child Family Institute for Innovation and Entrepreneurship serves as the nexus for entrepreneurship education and research — and as a springboard for entrepreneurial initiatives on the UC Davis campus. To accomplish this, the institute brings science, engineering and business students and faculty together with experienced entrepreneurs, investors and corporate leaders in a highly collaborative environment that blends effective theory with hands-on participation and solution-driven innovation.

Under the direction of Professor Andrew Hargadon, the institute provides researchers, MBA students and others with the necessary skills, resources and network support to turn their ideas into action. Whether for profit or for social benefit — or both — the institute’s programs enable students to envision a better world and make it a reality.

The Child Family Institute for Innovation and Entrepreneurship is a Center of Excellence at the Graduate School of Management.

H1N1 discovered in marine mammals

Wed, 15 May 2013 14:25:00 -0700

Scientists at the University of California, Davis, detected the H1N1 (2009) virus in free-ranging northern elephant seals off the central California coast a year after the human pandemic began, according to a study published today, May 15, in the journal PLOS ONE. It is the first report of that flu strain in any marine mammal.

“We thought we might find influenza viruses, which have been found before in marine mammals, but we did not expect to find pandemic H1N1,” said lead author Tracey Goldstein, an associate professor with the UC Davis One Health Institute and Wildlife Health Center. “This shows influenza viruses can move among species.”

UC Davis researchers have been studying flu viruses in wild birds and mammals since 2007 as part of the Centers of Excellence in Influenza Research and Surveillance program funded by National Institutes of Health. The goal of this research is to understand how viruses emerge and move among animals and people.

Between 2009 and 2011, the team of scientists tested nasal swabs from more than 900 marine mammals from 10 different species off the Pacific Coast from Alaska to California. They detected H1N1 infection in two northern elephant seals and antibodies to the virus in an additional 28 elephant seals, indicating more widespread exposure.

Neither infected seal appeared to be ill, indicating marine mammals may be infected without showing clinical signs of illness.

The findings are particularly pertinent to people who handle marine mammals, such as veterinarians and animal rescue and rehabilitation workers, Goldstein said. They are also a reminder of the importance of wearing personal protective gear when working around marine mammals, both to prevent workers’ exposure to diseases, as well as to prevent the transmission of human diseases to animals.

H1N1 originated in pigs. It emerged in humans in 2009, spreading worldwide as a pandemic. The World Health Organization now considers the H1N1 strain from 2009 to be under control, taking on the behavior of a seasonal virus.

“H1N1 was circulating in humans in 2009,” said Goldstein. “The seals on land in early 2010 tested negative before they went to sea, but when they returned from sea in spring 2010, they tested positive. So the question is where did it come from?”

When elephant seals are at sea, they spend most of their time foraging in the northeast Pacific Ocean off the continental shelf, which makes direct contact with humans unlikely, the report said.

The seals had been satellite tagged and tracked, so the researchers knew exactly where they had been and when they arrived on the coast. The first seal traveled from California on Feb. 11 to southeast Alaska to forage off the continental shelf, returning to Point Piedras Blancas near San Simeon, Calif., on April 24. The second seal left Ano Nuevo State Reserve in San Mateo County, Calif., on Feb. 8, traveling to the northeast Pacific and returning on May 5. Infections in both seals were detected within days of their return to land. The report said exposure likely occurred in the seals before they reached land, either while at sea or upon entering the near-shore environment.

The research, led by scientists Goldstein and Walter Boyce at the UC Davis School of Veterinary Medicine’s One Health Institute, was conducted with collaborators Nacho Mena and Adolfo García-Sastre at the Icahn School of Medicine at Mount Sinai in New York, who sequenced the virus isolates and characterized their phenotypic properties.

“The study of influenza virus infections in unusual hosts, such as elephant seals, is likely to provide us with clues to understand the ability of influenza virus to jump from one host to another and initiate pandemics,” said García-Sastre, professor of microbiology and director of the Global Health and Emerging Pathogens Institute at the Icahn School of Medicine.

The research was funded primarily through the Centers of Excellence for Influenza Research and Surveillance, a program supported by the National Institute of Allergy and Infectious Disease, and the Tagging of Pacific Predators program, a project of the Census of Marine Life.

About the UC Davis School of Veterinary Medicine

As a top veterinary school internationally, and a leader in preventive medicine and wildlife health, UC Davis has an extensive research and training record in the fields of epidemiology, surveillance, zoonotic diseases, comparative medicine, diagnostics, wildlife pathogens and conservation, food safety, disease prevention and outbreak response. The school has trained more than 800 international veterinarians from 75 countries, including hot spots in Africa, Latin America and Asia. Its One Health Institute and Wildlife Health Center manage One Health programs for people and animals ranging from the Pacific Northwest to Africa’s Congo Basin and Rift Valley.

Talk: Mars Curiosity lead engineer returns to UC Davis

Tue, 14 May 2013 09:34:00 -0700

NASA Jet Propulsion Lab lead engineer Adam Steltzner, who became a highly visible presence during last year's Mars Curiosity Rover mission, will give a presentation at 4 p.m. Tuesday, May 21, in UC Davis' 1065 Kemper Hall. His talk is titled: "The Right Kind of Crazy: Risk, Reason and Engineering Curiosity to the Surface of Mars." Admission is free.

A graduate of UC Davis, Steltzner led the innovative Entry, Descent and Landing team that guided Curiosity to its successful touchdown inside Mars' massive Gale Crater on Aug. 5.

Steltzner and his team — at one point, almost 2,000 people — devised the rocket-powered "sky crane," which hovered over the planet's surface and gently lowered Curiosity on a cable.

Steltzner discusses the development of this unique landing system in NASA's "Seven Minutes of Terror," a short video that has become a YouTube sensation, with more than 2 million views. See: http://youtu.be/Ki_Af_o9Q9s.

Despite the acclaim that has followed his work on Curiosity, Steltzner almost didn't find his scientific muse: After a lackluster high school career, he wanted only to play bass and drums in various New Wave bands.

But one night in 1984, entranced by the constellation Orion while returning home from a gig, he embraced higher education with fresh enthusiasm. He earned a bachelor's degree in mechanical engineering at UC Davis in 1990, and followed that with a master's degree in applied mechanics from the California Institute of Technology and a doctorate from the University of Wisconsin.

His early projects with JPL's Spacecraft Structures and Dynamics Group included the Galileo and Cassini space probes, Mars Pathfinder and the Mars Exploration Rovers Spirit and Opportunity.

For additional information, call (530) 754-9666 or visit http://engineering.ucdavis.edu.

Geneticist appointed as Hughes investigator

Thu, 09 May 2013 10:05:00 -0700

Neil Hunter, a professor of microbiology and molecular genetics at the University of California, Davis, College of Biological Sciences, has been named as a Howard Hughes Medical Institute investigator, an honor reserved for scientists who exhibit exceptionally original thinking. Hunter studies the most fundamental processes of how genes are shuffled and passed to the next generation.

The HHMI will pay Hunter's salary and research laboratory expenses, including salaries for research staff, for five years. He will then have an opportunity to apply for renewal of the grant.

"I'm delighted to congratulate Professor Hunter on this appointment, which underlines the growing prestige and influence of UC Davis as a center for biomedical research," said UC Davis Chancellor Linda P.B. Katehi.

Hunter is the first UC Davis faculty member to be appointed to the prestigious HHMI Investigator program and one of just 27 new HHMI investigators announced today (May 9) from a field of 1,155 applicants. In 2009, Hunter was named an early career scientist by the institute.

"Being named as an HHMI investigator is an exceptional honor for Neil, as well as for the UC Davis College of Biological Sciences," said James E. K. Hildreth, dean of the college. "He is a leader in the field of DNA recombination and his research has major implications for understanding many diseases, including cancer. Support from HHMI will allow him to sustain his research excellence for many years to come."

Robert Tjian, HHMI president, said the organization has a very simple mission. "We find the best original-thinking scientists and give them the resources to follow their instincts in discovering basic biological processes that may one day lead to better medical outcomes," Tjian said.

Under the terms of the award, Hunter will be an employee of HHMI working at UC Davis. There are approximately 330 HHMI investigators in the U.S. who are urged to "take risks, to explore unproven avenues, and to embrace the unknown — even if it means uncertainty or the chance of failure," according to the institute's website. There are no annual reports, and investigators are free to explore and change their research direction.

Hunter said that being affiliated with HHMI has been one of the most rewarding experiences of his scientific career, and thanked those who have helped him along the way. "I would not have received this honor without the understanding, encouragement and support of my family, colleagues, department chairs and deans, both past and present," he said.

HHMI investigators are expected to devote about three-quarters of their time to research, but also to participate in other faculty duties including teaching and service.

Hunter is studying a fundamental problem in biology: how cells shuffle their DNA and distribute exactly the right number of chromosomes to each sperm or egg cell. When cells divide to make sperm and eggs, how do they make sure that each cell obtains one full set of chromosomes?

When this process goes wrong, it can lead to miscarriage and developmental defects such as Down syndrome. It is estimated that around half of the roughly 1 million miscarriages that occur in the U.S. each year are due to a chromosomal imbalance. The risk increases with the mother's age.

Organisms from yeast to humans make their gametes (spores in yeast, sperm and eggs in humans) through a process called meiosis. While most body cells contain pairs of each chromosome, sperm and eggs have one copy of each, so that the fertilized egg ends up with one set of chromosomes from each parent.

During meiosis, the matching pairs of maternal and paternal chromosomes line up together, and their DNA strands interact by a process called recombination. This allows the chromosomes to exchange DNA with their paired partner, an event called a crossover.

"Initially there are hundreds of DNA breaks throughout the chromosomes, but only a few become crossovers," Hunter said.

Crucially, there has to be at least one crossover between each chromosome pair, or they will not line up properly, and gametes will receive the wrong number of chromosomes.

"I'm interested in how crossovers are made — how the process is wired in such a way that each pair of chromosomes always gets at least one crossover, even through the total number of crossovers in a cell is quite low. It's a fundamental process that we’re far from understanding," Hunter said. The crossover process was first proposed in 1909 by Belgian scientist Frans Janssens, who observed crossovers in cells undergoing meiosis from the Californian salamander.

Hunter is also a member of the UC Davis Comprehensive Cancer Center. In 2011, two UC Davis plant biologists, Professor Jorge Dubcovsky, Department of Plant Sciences, and the late Simon Chan, Department of Plant Biology, were among the first-ever class of HHMI-GBMF investigators, funded jointly by the Howard Hughes Medical Institute and the Gordon and Betty Moore Foundation to support research leading to improved crops.

UC Davis ranks No. 1 in the world for agricultural teaching and research

Wed, 08 May 2013 08:30:00 -0700

The University of California, Davis, is No. 1 in the world for teaching and research in the area of agriculture and forestry, according to rankings released today by QS World University Rankings.

This is the first year that the organization — which provides annual rankings in 29 other subject areas — has produced rankings in agriculture and forestry.

UC Davis this year also placed 12th in environmental sciences and 25th in biological sciences in the worldwide university ranking. Both of these subject-area rankings reflect significant advances from 2012, when UC Davis ranked 39th in biological sciences and below the top 50 institutions in environmental sciences.

“We are thrilled and excited by this evaluation, and it is gratifying to see that the ranking data validate the breadth and depth of our agricultural programs, which represent a variety of disciplines,” said Mary Delany, interim dean of the College of Agricultural and Environmental Sciences.

“At the institutional level, this ranking signifies rich teaching and research programs that developed and were built during our more than 100 years of service,” she said. “And at the personal level, it reflects the devotion of more than 300 faculty members who are passionate about their fundamental, translational and applied research, and thoroughly devoted to training the next generation of scientists and agriculturalists.”

The college was founded in 1905 as the University of California’s University Farm. Today, it has more than 5,800 undergraduate students in 27 majors and more than 1,000 graduate students in 45 graduate groups and programs. More than 3,000 acres of UC Davis’ 5,000-acre campus are devoted to agricultural research.

Its programs have characteristically received top-tier rankings from the Chronicle of Higher Education, U.S. News and World Report and ISI Essential Science Indicators.

UC Davis, overall, ranked eighth among public research universities nationwide in the U.S. News & World Reports’ 2013 America’s Best Colleges rankings.

The QS World University Rankings by Subject are prepared by Quacquarelli Symonds (QS), a British firm that previously was the data provider for the annual Times Higher Education rankings. The firm is widely considered to be one of the most influential international university rankings providers. This is the third year it has produced its own world university rankings, independent of the Times Higher Education World University Rankings.

For this third edition of the QS World University Rankings by Subject, the firm evaluated 2,858 universities and ranked 678 of those institutions in 30 subject areas.

Previously, it used three measures to rank universities within subject areas: the number of times research publications from the institution were cited by other researchers in professional journals, opinions of other academics in the field and opinions of employers in the field.

This year, the organization added a fourth ranking measure — the H-index — which measures the number of research papers published as well as the number of times those papers have been cited by other researchers, thus rewarding both the quantity and quality of research.

One big European family (WITH VIDEO)

Tue, 07 May 2013 14:05:00 -0700

From Ireland to the Balkans, Europeans are basically one big family, closely related to one another for the past thousand years, according to a new study of the DNA of people from across the continent.

The study, co-authored by Graham Coop, a professor of evolution and ecology at the University of California, Davis, is published May 7 in the journal PLoS Biology.

"What’s remarkable about this is how closely everyone is related to each other. On a genealogical level, everyone in Europe traces back to nearly the same set of ancestors only a thousand years ago," Coop said.

"This was predicted in theory over a decade ago, and we now have concrete evidence from DNA data," Coop said, adding that such close kinship likely exists in other parts of the world as well.

Coop and co-author Peter Ralph, now a professor at the University of Southern California, set out to study relatedness among Europeans in recent history, up to about 3,000 years ago. Drawing on the Population Reference Sample (POPRES) database, a resource for population and genetics research, they compared genetic sequences from more than 2,000 individuals.

As expected, Coop and Ralph found that the degree of genetic relatedness between two people tends to be smaller the farther apart they live. But even a pair of individuals who live as far apart as the United Kingdom and Turkey — a distance of some 2,000 miles — likely are related to all of one another's ancestors from a thousand years ago.

Subtle local differences, which likely mark demographic shifts and historic migrations, exist on top of this underlying kinship, Ralph said. Barriers like mountain ranges and linguistic differences have also slightly reduced relatedness among regions.

Coop noted, however, that these are all relatively small differences.

"The overall picture is that everybody is related, and we are looking at only subtle differences between regions," he said.

To learn about these patterns, Ralph and Coop used ideas about the expected amount of genome shared between relatives of varying degrees of relatedness. For example, first cousins have grandparents in common and share long stretches of DNA.

Ralph and Coop looked for shorter blocks of DNA that were shared between cousins separated by many more generations.

Because the number of ancestors doubles with every generation, the chance of having identical DNA in common with more distant relatives quickly drops. But in large samples, rare cases of distant sharing could be detected. With their analysis, Coop and Ralph were able to detect these shared blocks of DNA in individuals spread across Europe, and calculate how long ago they shared an ancestor.

Coop and Ralph hope to continue the work with larger and more detailed databases, including much finer-resolution data on where individuals lived within a country.

However, Coop noted that while studies of genetic ancestry can shed light on history, they do not tell the whole story. Archaeology and linguistics also provide important information about how cultures and societies move and change.

"These studies need to proceed hand in hand, to form a much fuller picture of history," Coop said.

Researchers propose tool to improve stream habitat in California’s Scott River

Mon, 06 May 2013 10:25:00 -0700

A team of University of California, Davis, scientists is developing a groundwater management tool that could lead to better streamflow conditions for salmon and steelhead in northern California’s Scott River Valley, which provides critical fish habitat within the Klamath Basin.

This mountain valley also supports an agricultural economy composed of small family farms and ranches, raising alfalfa hay, pasture, and cattle. Regulatory agencies, farmers, ranchers and the local community are working to find win-win solutions for both fish habitat and agriculture.

“For most other rivers in California, summer and fall water flows are entirely dictated by dams that have water behind them,” said Thomas Harter, a Cooperative Extension groundwater hydrologist in the Department of Land, Air and Water Resources who led the study. “Scott River is very dependent on the groundwater system."

The 57-mile-long, undammed Scott River is a tributary of the Klamath River, and portions of it are designated as a federal and state Wild and Scenic River. A combination of irrigated agriculture in Scott River Valley, a lack of streamside shade on the river, and climate change has led to warmer river temperatures and reduced late summer and fall stream flows on the river, particularly in dry years, Harter said.

In a recent report to the North Coast Regional Water Quality Control Board, the researchers summarized the hydrology of the Scott Valley, gathering data about rainfall, climate, soils, land use, irrigation and groundwater flows distributed across the basin for the past 21 years. Harter will combine this information into an integrated hydrologic model, expected to be complete in early 2014.

Scott Valley is addressing the issue on multiple frontiers, including riparian management and the recent development of a groundwater management plan. The UC Davis tool will be used to evaluate future groundwater management scenarios, which could include: How do irrigation management practices affect flow and temperature in the river? What are the effects of allowing for more beaver dams? How can additional water recharge during spring and early summer be used to support the aquifer during the critical late summer period?

“The local community and other stakeholders have a number of ideas on groundwater management that could benefit the stream flow,” Harter said. “This hydrologic model will provide the physical framework to evaluate those ideas. It will provide guidance on the possible direction that groundwater management can take in the Scott Valley.”

The hydrologic tool could help inform decision-makers and regulatory agencies involved in the issue of balancing salmon protection and water management along the Scott River.

As agencies, decision-makers, farmers, fishermen, and the public grapple with the questions posed by a changing climate and a changing river, the UC Davis hydrologic tool is expected to help provide science-based answers.

Background

The North Coast Regional Water Quality Control Board adopted a Total Maximum Daily Load implementation program pursuant to the Clean Water Act. The program requested Siskiyou County develop a groundwater study plan to understand how surface water temperature might be made cooler through its connection with groundwater. The county approached Harter to oversee the development of the plan, which was funded by the board and adopted by the county in 2008. The county Board of Supervisors established the Scott Valley Groundwater Advisory Committee in 2011 to address groundwater issues. The committee served as a resource for the new report, which is part of the original study plan effort and was also funded by the North Coast Regional Water Quality Control Board.